view xenaGetDataset.xml @ 55:421b18a0b659 default tip

update v17 step 2, add xena.jar

<tool id="xenaGetDataset"  name="Get Data from Xena" version="0.0.2">
  <description>
    Download individual dataset from the federated Xena platfrom
  </description>
  <requirements>
    <requirement type="package" version="1.0">installXena</requirement>
  </requirements>
  <command interpreter="python">
    #if $hub.dataHub == "https://genome-cancer.ucsc.edu/proj/public/xena":
        xenaGetDataset.py $hub.dataHub $dataset $dataFile $GALAXY_URL
    #elif $hub.customDataHub:
        getXenaData.py $hub.customDataHub $dataset $dataFile $GALAXY_URL
    #else
        getXenaData.py $hub.dataHub $dataset $dataFile $GALAXY_URL
    #end if
  </command>
  <inputs>
    <conditional name="hub">
      <param type="select" name="dataHub" label="Data Hub" optional="false">
	<option value="https://genome-cancer.ucsc.edu/proj/public/xena"/>
	<option value="datahub">Enter a different hub</option>
      </param>
      <when value ="https://genome-cancer.ucsc.edu/proj/public/xena"/>
      <when value ="datahub">
	<param type="text" name ="customDataHub" label="Hub url" optional="false"/>
      </when>
    </conditional>  
    <param type="text" name="dataset" label="Dataset ID" optional="false" help="How do I find the dataset ID? Tools section-> UCSC Xena Platform ->  Explore Data in Xena:  It takes you to the xena data exploration page. Browser to find the cohort of your interest (e.g. TCGA Lung Adenocarcinoma), then click the cohort link, then find the dataset of your interest (e.g. LUAD exon expression (IlluminaHiSeq) ), click the dataset link to go to its own detailed page. Copy and paste from the dataset ID field." />    
    <param name="GALAXY_URL" type="baseurl" />
  </inputs>
  <outputs>
    <data format="tabular" name="dataFile" label="${dataset}" />
  </outputs>
  <stdio>
    <exit_code range="1"   level="fatal"   description="Click the eyeball icon to see details." />
    <exit_code range="2"   level="fatal"   description="Not enough input arguments" />
  </stdio>
  <help>
    Given the data hub name and the dataset id, download the dataset into this Galaxy. Xena dataset id can be obtained through the Explore Data in Xena tool.
  </help>
</tool>